To function properly, the cell cytoskeleton undergoes tightly orchestrated changes in organization at the submicron level, particularly at the periphery. Despite many studies, there are major gaps in our understanding of the mechanisms that affect and control cytoskeletal organization and function, due primarily to inability to examine the detailed mechanical properties of the cell. The most commonly used technique for studying cells, indirect immunofluorescence and electron microscopy, are insufficient because (1) they have inadequate temporal and spatial resolution and (2) they provide only structural information. Both dynamical structural and functional data at the submicron level are required to fully understand how cells work. Previous measurements of cell stiffness also did not have the required spatial resolution. One promising new method is nano-identification using atomic force microscopy (AFM). Since its invention 10 years ago, AFM has become recognized as a potentially useful tool for studying regional properties in living cells. However, all existing studies of biological materials have analyzed AFM data based on equations derived assuming infinitesimally small deformations, linear elasticity, and homogeneity. None of these assumptions are likely to pertain to biological structures. Hence, the estimates of cell stiffness in the literature are almost certainly wrong. Our goal is to develop a systematic approach to address some critical methodological issues related to AFM, such as how to better calibrate the cantilevers and how to better understand the mechanics of indentation with pyramidal-shaped tips. We propose to use finite-element methods of structural analyses to tackle these problems. We will specifically focus on the conditions under which linear elasticity theory can and can not be applied to the finite-deformation mechanics of indentation. We will also investigate how and if heterogeneity of mechanical properties can be assessed by indentation. These studies will serve both as guidelines for indentation studies as well as a foundation for reliable analyses for future indentation results. Once these goals are achieved, we will have the tools to begin answering some crucial questions about cell function using AFM.